1. Field of Invention
This invention concerns a novel marker for human immunodeficiency virus (HIV) latency and a method for detection and monitoring of HIV activation. The assay sensitively detects HIV transcription and monitors HIV transcriptional activity by detecting the presence of short TAR fragments and full length transcripts, quantifying both and determining the ratio of short to long transcripts. In particular, the invention utilizes the discovery that a unique short RNA transcript, the transactivator response element (TAR), is present in abundance in the peripheral blood mononuclear cells of (PBMC) of asymptomatic HIV subjects. The abundance of these TAR fragments make them a good marker for the presence of virus and the ratio of these TAR fragments to full-length transcripts correlates well with increased processive transcriptional activity of HIV leading to increased replication of the virus. The size difference between the TAR fragments, appearing predominantly in latency, and the full length transcripts appearing predominantly during HIV activation, is detected by RT-PCR utilizing novel primers and probes and expressed as a ratio of short to long transcripts. The obtained ratio is a sensitive tool in detection of HIV infection, is a unique tool for determining the load of latent and active virus, and is useful for monitoring the transition from the latent to active state of HIV replication. The assay detects the presence of TAR fragments and full length transcripts, quantifies both and determines the ratio of short to long transcripts.